Now this may be stupid, but to me, right now, I would rather learn more about linux and python than java and windows. In 3 - 5 years I would like to be a python wizard, not a java wizard. Is that short-sighted?
The good news is that all these skills are transferable. Becoming a better Java programmer automatically makes you a better Python programmer, and vice versa.
What isn't transferable is domain knowledge. If you want to make something of yourself in this industry, you need to specialise in something. Learn everything there is to know about something, be it networking, writing compilers/virtual machines, security or operating system design, etc. If you don't, you're essentially doomed to a career of moving bytes from a to b, applying some trivial transform to them on the way. Which, incidentally, describes neatly the vast majority of web development.
would there be chance for you to transition into doing linux/python stuff over at ibm (they certainly do a great deal of linux/python work)? ask them that up front.
also what matters a lot more than the tools/languages/systems you will be working on is -- if you want to do core software developlment -- whether you will be working on company's bread and butter or something which is only tangential and "nice to have"? are you going to be doing new development or merely fixing bugs (or doing operations)?